Binding Site Visualization
Options for visualizing binding sites have been added to the Jmol options available at rcsb.org.
From a Structure Summary page (example: 1stp), select the option for "3D View" listed under the entry's image (or from the 3D View tab).
Options for viewing domains and ligands are at the bottom of the page.
Select the Ligand tab and then the link to "View Pocket in Jmol" to access this new feature. Residues are displayed in contact with the selected ligand. A cropped ligand van der Waals surface will appear that is color coded by the proximity to the van der Waals surface of the binding site (red: close contact, blue: far contact).
Thanks to Robert Hanson (St. Olaf College), the current principal Jmol developer, for implementing this feature during his visit to the RCSB PDB.